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Author: Lynnaun Johnson

Lynnaun Johnson is a Ph.D. student in the joint Plant Biology and Conservation program at Northwestern University and the Chicago Botanic Garden. He is interested in studying the microbes (fungi and bacteria) associated with orchid roots. He is particularly interested in the mutualistic relationships of these organisms.

Vanilla cookies, vanilla perfume, and everything vanilla swept through my nostrils at a scented display at last year’s Orchid Show. The sweet smell was a great way to show many visitors that vanilla comes from the fruits of the vanilla orchid (Vanilla planifolia).

What are the scribbles about? Orchid pods are dated to estimate how long the pods have been on the vine, possibly to determine a good time to harvest them.

As a docent at last year’s show, I was eager to show off the Garden’s vanilla plant (located in the Tropical Greenhouse next to the banana trees), because I knew that may visitors didn’t know that they had an orchid in their spice cabinet.

Currently, I am in the second year of my research of the vanilla orchid. Vanilla is an exciting plant to study because it grows as a vine with two different types of roots. These roots help vanilla grow as a vine (more precisely a hemiepiphyte) because terrestrial roots anchor it within the soil, and epiphytic roots anchor it to tree trunks. My last post, Vanilla inhabitants: The search for associated bacteria and fungi, showcased my ongoing experiment in Mexico. This included collecting roots from four different Mexican farms that had very different practices for how they grew the orchid. We know that vanilla orchids use their epiphytic roots for support, but what other functions do they perform? Do they also form symbiotic relationships with fungal partners to obtain nutrients and water, like terrestrial roots?

Monocultures—crops with genetically identical heritage—are common in vanilla cultivation.

Many vanilla plantations use man-made structures for the vining orchids. Here, an old tree provides support to this orchid.

The fungal partners of orchids, known as mycorrhizal fungi, help an orchid start its life by providing needed nutrients for its seeds to germinate. No orchids in the wild can germinate without one or more mycorrhizal fungi. As a scientist, my goal is to study the interactions that the vanilla orchid has with these fungi as they mature. This is important because most vanilla farms are monocultures—it is easier to obtain clones from cuttings of vanilla than to germinate them from seeds. This, however, creates serious problems, because farms that have low genetic diversity in their vanilla orchids can lose their entire crop if a disease (such as root rot caused by Fusarium) appears.

Prior reports based on classic techniques have documented two or three species of mycorrhizal fungi within vanilla roots. In addition to these mycorrhizal fungi, there are also fungal pathogens (fungi that cause disease) and fungal endophytes (fungi that seem to have a mutualistic relationship with the host) that colonize a vanilla’s root.

To further investigate the situation, I ran an experiment using the latest DNA technology—Next Generation Sequencing (NGS)—to document the communities of fungi within terrestrial and epiphytic vanilla roots.

As fungal endophytes take up nutrients from their host, the mycotoxins they produce reduce herbivory and susceptibility to pathogens.

A length of canopies shields the growing vanilla orchids from harsh direct sunlight.

I documented 142 species of fungi associated with vanilla roots from the four Mexican farms, with an average of nine fungi colonizing a single vanilla root at one time. Of these 142 species, 20 are likely mycorrhizal. I find that fascinating, because these mycorrhizal fungi were found within both root types and across all farms. It was also surprising to know that epiphytic roots have a similar diversity of mycorrhizal fungi as terrestrial roots even though the epiphytic roots were green and could photosynthesize and have been considered primarily as support structures.

My study also documented a high number of previously unreported species of fungal pathogens and fungal endophytes colonized the roots of vanilla plants. This means that if plants are unhealthy, fungal pathogens likely can quickly take over, because they are already present within the roots. Overall, vanilla roots have good and bad partners just like we do, but contain more beneficial fungi (fungal endophytes and mycorrhizal fungi) than previously believed. These beneficial fungi not only supply the plant with water and nutrients, but also help control fungal pathogens. Thus, they are essential for plant health.

This research is funded with support from Mexican collaborators as part of the SAGARPA-CONACYT-SNITT 2012-04-190442 Mexican Vanilla Project.

Learn more about the orchids in your kitchen cabinet with our Vanilla Infographic; read up on another edible orchid in A Sip of Salep. Stay tuned for more orchid research projects, amazing orchid displays, and fun facts on our blog. The Orchid Show opens February 13!

For this year’s Orchid Show, we’ve gathered stories about the most famous orchid of them all: the genus Vanilla. (Yes, vanilla is an orchid.) One unusual story comes from Ph.D. student Lynnaun Johnson, whose work in our doctoral program in Plant Biology and Conservation took him to Mexico, the native land of edible vanilla.

Last April, I ventured to Mexico as part of an international team investigating how cultivation practices influence the growth and health of the orchid Vanilla planifolia.

Vanilla planifolia produces the seedpods used to make vanilla, the spice used for flavoring desserts and beverages, and for providing wonderful aromas in candles, perfumes, and many other things. This collection trip would take me to vanilla’s native habitat of Mexico. All varieties of vanilla originated in Mexico, including those of Madagascar and Tahiti.

While in Mexico, I visited three farms in the state of Veracruz and one in the state of Puebla. It was fascinating driving to these vanilla farms with my Mexican collaborators. It took us three days of traveling to complete our field collections. Each of the four farms had very different methods of growing V. planifolia. For instance, one of the farmers said he knew what his plants needed and thought growing his vanilla on concrete blocks was the best method. At another farm, the farmer brought decaying wood from a neighboring forest and used it as mulch for his vanilla plants that grew on living posts known as “tuteurs.” This was different from the other farmers who grew their vanilla on trees in the forest and wooden dead “tuteurs.”

Each of the plantations had different soil texture. At the last organic farm, the soil was compact and hard. At the farms that were in the forest, the soil appeared rich and softer. There is no way to quantify the terrestrial root growth, but I did note that the roots in the organic farms were longer and healthier, with some growing up to 4 or 5 feet when we dug the roots up from the soil.

At the Pantapec farm in the state of Puebla, Mexico, vanilla is cultivated in a highly managed environment.

By contrast, the vanilla grown at 1 de Mayo farm in the state of Veracruz, Mexico, is cultivated in a completely natural environment.

The benefits of fungi

Research on rare and endangered orchids usually focuses on finding fungi to help in the germination of orchids. We know that orchids will only germinate in nature using fungi. In addition, fungi living inside of plant leaves can benefit the plants’ health by preventing pathogens from growing. Also, bacteria living within the plants and fungi can be beneficial in the same way as the endophytic fungi. (Photo: V. planifolia tissue microscopy at 100x)

My part of the research project is to collect root samples from V. planifolia from each of these different farms to study the fungi and bacteria inhabiting this orchid. Currently, not much is known about the microbes (fungi and bacteria) that reside in orchid roots. Some fungi and bacteria can cause diseases. For example, with the appearance of a fungal pathogen such as Fusarium oxysporum, Mexican farmers can lose 67 percent of their crops when the Fusarium causes the rotting of the Vanilla’s stem and roots. On the other hand, there are beneficial fungi that inhabit roots, known as mycorrhizal fungi. These beneficial symbiotic fungi acquire mineral nutrients for the Vanilla, and sometimes receive carbon from the orchid in exchange. Although 90 percent of plant species have mycorrhizal fungi, and while we have a good understanding of mycorrhizal fungi of some of these relationships, relatively little is known about the mycorrhizal fungi of orchids, including V. planifolia. The reason for this is that isolating and growing the fungi and bacteria associated with orchid roots can be difficult, and some have never been grown outside of their host.

At each farm, I wanted to sample five individual plants of V. planifolia. Additionally, because of the lifestyle of this orchid, I also wanted to sample the above-ground roots (epiphytic) and the below-ground (terrestrial) roots in the soil. Using either a scissors or a scalpel, I cut small root samples and placed them into Ziploc bags. The vanilla plants are very precious to the farmers, and so a few were initially uncomfortable with our cutting off pieces, but ultimately they were very accommodating.

Epiphytic or terrestrial?

Typically, vanilla grows as a vine, with two types of roots: epiphytic roots (those that wrap around trees or other structures) and terrestrial (soil) roots. This is referred to as hemiepiphytic, because it starts in the ground and grows upward onto the tree’s bark. Many research papers suggest that epiphytic roots do not harbor many fungi, because these roots can photosynthesize, and do not need mutualistic fungus partners.

Back here at the Chicago Botanic Garden, I am in the process of evaluating the microbial community that lives in the root samples I collected. We are using a new technique called high-throughput sequencing that will enable me to evaluate the entire fungal and bacterial community within the orchid’s roots by using their DNA as a way to fingerprint the individual species of microbes. We are not certain how many species of fungi and bacteria we will find, but we predict that this method will give us a good picture of the fungal and bacterial community in these roots and if these communities differ among the different farming techniques. These data will be used to better understand how epiphytic orchids utilize mycorrhizal fungi and refine the best conditions to grow vanilla and prevent diseases in the plants.

This research trip was a delight, not only because of the samples that I collected, but also because I could learn more about how vanilla is grown and used. The farmers showed us how they cure and prepare the vanilla by fermenting it in the sun and before drying it thoroughly. I also tasted homemade “vanilla moonshine,” generously offered by the farmer’s wife. When visiting Papantla, I learned about the Aztec myth that explained how forbidden love created the sacred vanilla orchid. And of course, I was elated because I usually spend the majority of my research time in the lab. And here I was in the tropics, after spending the previous months facing the bitter Chicago 2014 winter.